On Friday afternoon Perez qualified third for the Spa-Francorchamps race, behind team-mate Max Verstappen and Ferrari's Charles Leclerc.
After Perez's final qualifying lap team principal Christian Horner came on the radio to congratulate the Mexican, who replied: "Ah, you will talk to me now..."
Horner replied: "I will talk to you. I said to you top five, mate. You've blitzed it."
The exchange began to take on a life of its own on social media, with fans speculating about a rift between Horner and his driver.
In Sunday's post-race press conference Perez explained the inside joke behind the exchange that was taken out of context.
"It was a joke," Perez said. "He came before qualifying and said: ‘if you're not in the top three, I will not talk to you the rest of the weekend’.
"So, he was talking to me the rest of the weekend."
When asked by Autosport to clarify the message, Horner quipped: "I told him that I wasn't going to talk to him if he wasn't in the top five and I would squeeze a part of his anatomy if he wasn't.
"It seemed to do the job, so we'll have to try that again in Zandvoort..."
The qualifying result was somewhat of a return to form for Perez after failing to reach the Q3 shootout for five races in a row and only managing ninth in Hungary.
Perez went on to finish second in Sunday's race after being passed by the dominant Verstappen before the halfway mark.
Horner believes the Spa result will allow Perez to go into the summer shutdown with much more belief after seeing several weekends derailed and having witnessed Verstappen run away with the drivers' championship.
"I think he'll have taken a lot more confidence out of this weekend," Horner added.
"He put it on the front row. He led the grand prix, finished second, he's a clear second in the drivers' world championship, so I think he'll take some confidence out of it.
"I think that Checo knows that barring a disaster for Max that this championship is out of reach.
"So, it's about him maximising his own performance, not losing ground to any of the drivers behind and trying to pick up a few wins between now and the end of the year."
Additional reporting by Alex Kalinauckas
